Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.     

Ab initio computed diabatic potential energy surfaces of OH-HCl

The two four-dimensional diabatic potential energy surfaces (DPESs) for OH-HCl are computed that correlate with the twofold degenerate (2)Pi ground state of the free OH radical. About 20 000 points on the surface are obtained by the ab initio coupled-cluster and multi-reference configuration interaction methods. Analytic forms for the diabatic potential energy surfaces are derived as expansions in complete sets of orthogonal functions depending on the three intermolecular angles. The numeric computation of the angular expansion coefficients is discussed. The distance-dependence of the angular coefficients is represented by the reproducing kernel Hilbert space method. It is checked that both diabatic potentials converge for large intermolecular separations to the values computed directly from the electrostatic multipole expansion. The final DPESs are discussed and illustrated by some physically meaningful one- and two-dimensional cuts through them.     

Ab initio potential energy and dipole moment surfaces for H5O2 +

Full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) are reported for H(5)O(2) (+). Tens of thousands of coupled-cluster [CCSD(T)] and second-order Moller-Plesset (MP2) calculations of electronic energies, using aug-cc-pVTZ basis, were done. The energies were fit very precisely in terms of all the internuclear distances, using standard least-square procedures, however, with a fitting basis that satisfies permutational symmetry with respect to like atoms. The H(5)O(2) (+) PES is a fit to 48 189 CCSD(T) energies, containing 7962 polynomial coefficients. The PES has a rms fitting error of 34.9 cm(-1) for the entire data set up to 110 000 cm(-1). This surface can describe various internal floppy motions, including the H atom exchanges, monomer inversions, and monomer torsions. First- and higher-order saddle points have been located on the surface and compared with available previous theoretical work. In addition, the PES dissociates correctly (and symmetrically) to H(2)O+H(3)O(+), with D(e)=11 923.8 cm(-1). Geometrical and vibrational properties of the monomer fragments are presented. The corresponding global DMS fit (MP2 based) involves 3844 polynomial coefficients and also dissociates correctly.     

Ab initio calculations of many-body energy expansion in LiF− clusters

The effects of the basis-set size on many-body energy expansion in LiF^? clusters are investigated and correlated with previously reported values on LiCl^? analogs. Coulomb and non-Coulomb energies in LiF^? at different configurations are also examined. Although at the minimal STO -3G basis V^na(3, 4) and V^na(4, 4) nonadditivity terms were the smallest in the D₃h configuration, they were the largest at the extended 6-311 ++G basis. V(m, n) terms where m = n ≥ 3 were found to be playing a small role in the chemistry and physics of LiF^? clusters compared with V(3, n) terms in LiCl^? clusters.     

Ab initio potential and dipole moment surfaces for water. II. Local-monomer calculations of the infrared spectra of water clusters

We employ recent flexible ab initio potential energy and dipole surfaces [Y. Wang, X. Huang, B. C. Shepler, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 134, 094509 (2011)] to the calculation of IR spectra of the intramolecular modes of water clusters. We use a quantum approach that begins with a partitioned normal-mode analysis of perturbed monomers, and then obtains solutions of the corresponding Schro?dinger equations for the fully coupled intramolecular modes of each perturbed monomer. For water clusters, these modes are the two stretches and the bend. This approach is tested against benchmark calculations for the water dimer and trimer and then applied to the water clusters (H(2)O)(n) for n = 6-10 and n = 20. Comparisons of the spectra are made with previous ab initio harmonic and empirical potential calculations and available experiments.     

Ab initio copper–water interaction potential for the simulation of aqueous solutions

A new ab initio effective two-body potential that aims at mimicking the average copper–water interaction energy of the first solvation shell was developed. This new potential, together with the MCY water–water potential and a three-body ion–water–water induction potential, is tested in simulations of gas-phase clusters [Cu²⁺? (H₂O)₂₀] and diluted solutions [Cu²⁺? (H₂O)₂₀₀] at T = 298 K. The results of simulations with conventional ab initio pair potentials, with and without three-body induction corrections, are also presented. The different types of copper–water interaction potentials are evaluated comparatively and the efficiency of the newly proposed effective pair potential is discussed. © 1993 John Wiley & Sons, Inc.     

Ab initio potential energy surfaces for BH+2

Preliminary ab initio calculations for the BH⁺₂ potential surface are presented. The reaction B⁺¹S) + H₂ → BH⁺ (B₂ (B²σ⁺) + H is shown to be most likely to occur for C_2v and near C_2v geometrics where there are avoided crossings between the 1 ¹A₁ and 2 ¹A₁ surfaces and between the 2 ¹A₁ and 3 ¹A₁ surfaces which should facilitate non-adiabatic transitions. Bent geometries are alos preferred for the reaction B⁺(¹S) + H₂ → BH⁺(A²π) + H for which there are avoided crossings in C₂ sysmmetry between surfaces correlating with 1 ¹A₁ and 1 ¹B₂ surfaces.     

Elucidating the role of many-body forces in liquid water. I. Simulations of water clusters on the VRT(ASP-W) potential surfaces

We test two new potentials for water, fit to vibration-rotation tunneling (VRT) data by employing diffusion quantum Monte Carlo simulations to calculate the vibrational ground-state properties of water clusters. These potentials, VRT(ASP-W)II and VRT(ASP-W)III, are fits of the highly detailed ASP-W (anisotropic site potential with Woermer dispersion) ab initio potential to (D(2)O)(2) microwave and far-infrared data, and along with the SAPT5s (five-site symmetry adapted perturbation theory) potentials, are the most accurate water dimer potential surfaces in the literature. The results from VRT(ASP-W)II and III are compared to those from the original ASP-W potential, the SAPT5s family of potentials, and several bulk water potentials. Only VRT(ASP-W)III and the spectroscopically "tuned" SAPT5st (with N-body induction included) accurately reproduce the vibrational ground-state structures of water clusters up to the hexamer. Finally, the importance of many-body induction and three-body dispersion are examined, and it is shown that the latter can have significant effects on water cluster properties despite its small magnitude.     

CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule

The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed.     

Ab initio potential energy and dipole moment surfaces of (H2O)2

A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) are reported for the water dimer, (H2O)2. The CCSD(T)-PES is a very precise fit to 19,805 ab initio energies obtained with the coupled-cluster (CCSD(T)) method, using an aug-cc-pVTZ basis. The standard counterpoise correction was applied to approximately eliminate basis set superposition errors. The fit is based on an approach that incorporates the permutational symmetry of identical atoms [Huang, X.; Braams, B.; Bowman, J. M. J. Chem.Phys. 2005, 122, 044308]. The DMS is a fit to the dipole moment obtained with M?ller-Plesset (MP2) theory, using an aug-cc-pVTZ basis. The PES has an RMS fitting error of 31 cm(-1) for energies below 20,000 cm(-1), relative to the global minimum. This surface can describe various internal floppy motions, including various monomer inversions, and isomerization pathways. Ten characteristic stationary points have been located on the surface, four of which are transition structures and the rest are higher order saddle points. Their geometrical and vibrational properties are presented and compared with available previous theoretical work. The CCSD(T)-PES and MP2-DMS dissociate correctly (and symmetrically) to two H2O monomers, with D(e) = 1665.7 cm(-1) (19.93 kJ/mol). Accurate quantum calculations of the zero-point energy of the dimer (using diffusion Monte Carlo) and the monomers (using a vibrational configuration interaction approach) are reported, and these together with D(e) give a value of D0 of 1042 cm(-1) (12.44 kJ/mol). A best estimated value is 1130 cm(-1) (13.5 kJ/mol).     

Ab initio simulations of liquid electrolytes for energy conversion and storage

Understanding physicochemical properties of liquid electrolytes is essential for predicting and optimizing device performance for a wide variety of emerging energy technologies, including photoelectrochemical water splitting, supercapacitors, and batteries. In this work, we review recent progress and open challenges in predicting structural, dynamical, and electronic properties of the liquids using first-principles approaches. We briefly summarize the basic concepts of first-principles molecular dynamics (FPMD), and we discuss how FPMD methods have enriched our understanding of a number of liquids, including aqueous solutions, organic electrolytes and ionic liquids. We also discuss technical challenges in extending FPMD simulations to the study of liquid electrolytes in more complex environments, including the interface between electrolytes and electrodes, which is a key component in many energy storage and conversion systems.     

Ab initio study of the torsional potential energy surfaces of N2O3 and N2O4: origin of the torsional barriers

Intrinsic reaction coordinate (IRC) torsional potentials were calculated for N(2)O(4) and N(2)O(3) based on optimized B3LYP/aug-cc-pVDZ geometries of the respective 90 degrees -twisted saddle points. These potentials were refined by obtaining CCSD(T)aug-cc-pVXZ energies [in the complete basis set (CBS) limit] of points along the IRC. A comparison is made between these ab initio potentials and an analytical form based on a two-term cosine expansion in terms of the N-N dihedral angle. The shapes of these two potential curves are in close agreement. The torsional barriers in N(2)O(4) and N(2)O(3) obtained from the CCSD(T)/CBS//B3LYP/aug-cc-pVDZ calculations are 2333 and 1704 cm(-1), respectively. For N(2)O(4) the torsion fundamental frequency from the IRC potential is 87.06 cm(-1), which is in good agreement with the experimentally reported value of 81.73 cm(-1). However, in the case of N(2)O(3) the torsional frequency found from the IRC potential, 144 cm(-1), is considerably larger than the reported experimental values 63-76 cm(-1). Consistent with this discrepancy, the torsional barrier obtained from several different calculations, 1417-1718 cm(-1), is higher than the value of 350 cm(-1) deduced from experimental studies. It is suggested that the assignment of the torsional mode in N(2)O(3) should be reexamined. N(2)O(4) and N(2)O(3) exhibit strong hyperconjugative interactions of in-plane O lone pairs with the central N-N sigma* antibond. Hyperconjugative stabilization is somewhat stronger at the planar geometries because 1,4 interactions of lone pairs on cis O atoms promote delocalization of electrons into the N-N antibond. Calculations therefore suggest that the torsional barriers in these molecules arise principally from a combination of 1,4 interactions and hyperconjugation.     

Ab initio potential energy surfaces and nonadiabatic interactions in the H+ +NO collision system

Ab initio calculations on the H(+)+NO system have been carried out in Jacobi coordinates at the multireference configuration interaction level employing Dunning's correlation-consistent polarized valence triple zeta basis set to analyze the role of low-lying electronic excited states in influencing the collision dynamics relevant to the experimental collision energy range of 9.5-30 eV. The lowest two adiabatic potential energy surfaces, asymptotically correlating to H(+)+NO(X (2)Pi) and H((2)S)+NO(+)(X (1)Sigma(+)), have been obtained. Using ab initio procedures, the (radial) nonadiabatic couplings and the mixing angle between the lowest two electronic states (1 (2)A' and 2 (2)A') have been obtained to yield the corresponding quasidiabatic potential energy matrix. The strengths of the computed vibrational coupling matrix elements reflect a similar trend, as has been observed experimentally in the magnitudes of the state-to-state transition probability for the inelastic vibrational excitations [J. Krutein and F. Linder, J. Chem. Phys. 71, 559 (1979); F. A. Gianturco et al., J. Phys. B 14, 667 (1981)].     

Ab initio potential energy curve for CH bond dissociation in methane

Ab initio calculations on CH₄ → CH₃ + H were performed at the MP4/6-31G** level including all single, double triple and quadruple excitations. Although triple excitations have little effect on the dissociation energy, they are very important in the 2–3 Å range. The potential curve appears to rise more sharply than a Morse curve in this region. Correlation effects are not important for the HCH angle optimization.     

Ab initio potential energy surfaces, bound states, and electronic spectrum of the Ar-SH complex

New ab initio potential energy surfaces for the (2)Pi ground electronic state of the Ar-SH complex are presented, calculated at the RCCSD(T)/aug-cc-pV5Z level. Weakly bound rotation-vibration levels are calculated using coupled-channel methods that properly account for the coupling between the two electronic states. The resulting wave functions are analyzed and a new adiabatic approximation including spin-orbit coupling is proposed. The ground-state wave functions are combined with those obtained for the excited (2)Sigma(+) state [D. M. Hirst, R. J. Doyle, and S. R. Mackenzie, Phys. Chem. Chem. Phys. 6, 5463 (2004)] to produce transition dipole moments. Modeling the transition intensities as a combination of these dipole moments and calculated lifetime values [A. B. McCoy, J. Chem. Phys. 109, 170 (1998)] leads to a good representation of the experimental fluorescence excitation spectrum [M.-C. Yang, A. P. Salzberg, B.-C. Chang, C. C. Carter, and T. A. Miller, J. Chem. Phys. 98, 4301 (1993)].     

Ab initio ground- and excited-state intermolecular potential energy surfaces for the NO-Ne and NO-Ar van der Waals complexes

The ground- [NO(X(2)Π)] and excited-state [NO(A(2)Σ(+))] intermolecular potential energy surfaces (IPESs) of the NO-Ne and NO-Ar van der Waals complexes are evaluated using the RCCSD(T) spin-restricted coupled cluster method and d-aug-cc-pVQZ basis set extended with a set of 3s3p2d1f1g midbond functions. These bases are selected from the results of a systematic basis-set convergence study carried out for the NO(A(2)Σ(+))-Ar state. We fit the interaction energies to analytic functions and compare the results to those previously available. The NO-Ar (NO-Ne) IPESs are characterized by absolute minima of -120 and -75 cm(-1) (-58 and -5 cm(-1)) at the ground and first excited state, respectively, located close to the T-shaped geometries for the ground states and at linear dispositions in the case of the excited states. The potentials are further used in the evaluation of the rovibrational spectra of the complexes, and the results are compared to those available in the literature.     

Ab initio study of L-orientational defect in the hydrogen-bonded pattern of liquid water

Current status of the theory of orientational defects in H-bonded pattern of liquid water is briefly reviewed. Ab initio calculated water clusters from dimer to heptamer are thoroughly analyzed in terms of H-bonded pattern. New water heptamer structure of norbornane type is found via ab initio HF 6-311G** calculation. Its normal vibrations are properly assigned. Two ab initio water hexamers that refer to orientational defects are revealed. This is the first evidence of ab initio orientational defect in H-bonded patterns of water clusters. Some properties including normal vibrations of these defects, are studied.     

Ab initio potential energy surface and rovibrational spectrum of Ar-HCCCN

We report an ab initio intermolecular potential energy surface of the Ar-HCCCN complex using a supermolecular method. The calculations were performed using the fourth-order M?ller-Plesset theory with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The complex was found to have a planar T-shaped structure minimum and a linear minimum with the Ar atom facing the H atom. The T-shaped minimum is the global minimum with the well depth of 236.81 cm(-1). A potential barrier separating the two minima is located at R=5.57 A and theta=20.39 degrees with the height of 151.59 cm(-1). The two-dimensional discrete variable representation was employed to calculate the rovibrational energy levels for Ar-HCCCN. The rovibrational spectra including intensities for the ground state and the first excited intermolecular vibrational state are also presented. The results show that the spectra are mostly b-type (Delta K(a)=+/-1) transitions with weak a-type (Delta K(a)=0) transitions in structure, which are in good agreement with the recent experimental results [A. Huckauf, W. Jager, P. Botschwina, and R. Oswald, J. Chem. Phys. 119, 7749 (2003)].